Ghost in a Half-Shell
by Azure Umbra
Summary: People love mutants in 2065 A.D. – "Who are you? Who slips into my mutated body and whispers to my ghost?" (Story takes place in the TMNT 2012!verse with a "Ghost in the Shell"-like plot)
1. Noise

_**In the near future, corporate laboratories reach out across our world. Mutagen surges within the cells of almost all living things.**_

 _ **The advance of mutagenic modification, however, has not wiped out nations and species, as well as cultural and ethnic groups.**_

* * *

 **Location: New York City**

 **Time: Evening**

The night was live with the sounds of voices and vehicles as the city of New York went on with its unending routine. It had always been known by the world as 'the city that never sleeps,' and as technology progressed, it would proceed to be an even more sleepless city. Out of every city in the world, it stood nearly at the apex in the field of genetic engineering, architecture, and other technological achievements. There was also the account of an increased population with a vast array of physical diversity. When it came to all those qualities combined, this city stands at the top of the hierarchy of global society, though that spot is shared equally with Tokyo, Japan. The towering buildings of various cubes, rectangles, prisms, and cylinders were dressed in the colorful lights of animated advertisements, so much that they are almost holographic. Other designs that reflected the creativity of their builders were not limited by space, but were adapted to stand together with the older buildings at any level. Even gardens, preserves, playgrounds, and other institutions and settlements with wide open spaces could be found anywhere above ground-level.

However, what made New York truly unique was that a significant chunk of its citizens were mutants. While most of the world remained populated mainly by humans, New York was among the first cities to make history by elevating the citizenship status of mutants. Mutants of all species of various shapes and sizes walked the streets of this light-saturated metropolis. Ones that began life as animals could go out in public under the sky without fear of any sort of retribution. Even other humans were free to make the decision to become mutants, celebrating it as an optional, but brand new stage of life. Together, all of them provided the colorful diversity that allowed New York to make its title of "the world's cultural center" greater than it has ever been.

Inevitably and unfortunately, with its boundless diversity came less desirable elements. Even among the burgeoning skyscrapers and interwoven roads that stood one over the other in every direction, it could not erase all of its old imperfections but only veil them for a time. Truth be told, whether human or mutant, there are those who seek out the shadows as much as they take contentment in the light. That is why the innocent are indebted to those willing to stand guard in those shadows.

It was one night that two helicopters were flying overhead, passing over a ring of towers near Manhattan overlooking the Upper Bay, flying somewhere in the direction of Ellis and Liberty Island. On the edge of a rooftop of one tower, a young redheaded girl in a trench-coat was in a kneeling position, an expression of deep thought present on her face. At the moment, she was sifting through a torrent of voices that streamed through her mind all at once. Words over words in many different languages, voices that belonged to so many creatures of different flesh, the girl passed up each and every one of them until her concentration shifted to a louder and more distinguished man's voice that sounded like that of a lax authority figure.

 _"There's no need for concern. Our country is quite capable of covering its tracks."_

Another voice, one that sounded younger and more self-conscious like that of a younger man, spoke up, _"That's why you need me, right?"_

 _"Depends on how you look at it. At any rate, every specimen has its defects and I would think that a man of your capability could cure our problem."_

 _"You don't understand. We aren't even sure that Project 4522 really is defective. Originally, the purpose of this project was to-"_

 ** _"Major O'Neil. The Oroku-Division is in position and ready to move in. Major, are you there?"_**

 ** _"Yeah, I heard you, Raph."_**

 ** _"I'm surprised you can hear anything. What's with all that noise in your brain today?"_ **

The redhead fiddled with her short ponytail and emitted a faint sigh. "Just going through my routines."

The redheaded girl, or rather Major O'Neil, proceeded to stand up, keeping just a few inches away from the edge. She unbuttoned the hem on her coat and opened it to reveal a tracksuit underneath. Both the shirt and pants were completely black with a single yellow stripe going down the sides of both legs and sleeves. The sleeves were folded upward to reveal her forearms and the collar was slightly unbuttoned to show a hint of a white t-shirt.

* * *

"Don't you think there's gonna be trouble later if the Oroku guys find out we butt into their business?"

A stocky green humanoid turtle with a red mask around his eyes maintained a smug expression on his face. He answered his human partner casually while leaning on the inner wall of a large vehicle with one hand. "If Oroku actually catches the bastard, then all they can really do is deport him. Don't forget we're the Hamato-Division. We'll clean it up. We're the ones who get our hands dirty."

The human rolled his eyes at the red-masked turtle's answer. He appeared to wear almost black all over, perhaps to complement the black hair on his head; the attire was mainly comprised of a grey t-shirt with dark brown sleeves under a black sleeveless hoodie, along with grey denim pants, black and white shoes, and a black headband with intricate white patterns. Leaning back against the same wall his red-masked terrapin partner was on, he turned his head to another person sitting at a computer screen.

"It's time now. Let's move to the pickup point."

The giant vehicle that almost seemed like a subway car on monster truck wheels rumbled and rolled away from the curb.

* * *

Back on the rooftop, Major O'Neil finished packing in a few 4-pointed metal stars into a small pouch strapped to her leg before flipping the top closed. She stood back up for a short moment until she felt she was ready. Then, she slowly turned around and let gravity pull her down. Gracefully, she fell from the rooftop on her back and as she began to flip back from upside-down to upright, she maintained a focused expression. Her backflip occurred in an instant, and as she continued to fall, she threw out a line that grappled onto a nearby ledge.

* * *

Meanwhile within the building itself, black clad soldiers were making their way up to the floor where the meeting Major O'Neil spied on was taking place. The lax authority figure, who surprisingly looked more like a fat man in a suit, was busy helping himself to a chicken leg while sitting on his lounge chair. He still conversed with the other younger man, but he still appeared to show a little more investment in his pleasure. But he was interrupted as one of his suited bodyguards went up to him to whisper in his ear.

"What? The Foot here?" he exclaimed, causing the younger man next to him to rise off his seat in panic. The bodyguard, along with his other partner, crouched at the exit door and readied their guns. Giving each other a signal, they flipped the door open and fired their guns on the coming soldiers, even bringing down a few of them.

"Stop it!" the fat man yelled angrily, abruptly standing up. "Who told you to fire? Put your guns down now!" Upon these words being spoken, more of the black clad soldiers charged into the room through another existing pair of doors. The soldiers who weren't shot poured through the door the guards initially opened fire in and quickly subdued them. The fat man and his younger thinner compatriot were quickly surrounded, but the fat man wasted no time putting his authority to work. "I am Dominic Vizioso. I'm entitled to diplomatic immunity," he exclaimed, presenting them his identification while holding on to his chicken leg. "I want to talk to the person in charge here." Upon speaking these words, the soldiers parted to allow their leader to come through to meet him.

The leader in question appeared to be fairly tall. Unlike the fat man, he was thin, but at the same time, he was well-built. He wore a helmet that had a three-pronged adornment at the front, with a metal face plate covering all of his face except for his eyes attached to the helmet. He had a metallic breastplate that was covered in a scaly pattern and a pair of dark pants complementing his metallic boots. His upper arms were completely exposed while his forearms were fitted with gauntlets that held retractable blades. Anyone who'd look this man in the eyes might endure a terrified shiver as he exhumed an aura of harshness and a lack of compromise. Almost no one would be daring enough to test if his look was legitimately threatening or blusteringly extravagant on his part.

"Oroku Saki," the fat man muttered in recognition with an exasperatedly low voice.

"Taking classified geneticists out of the country compromises national security, Mr. Vizioso," the armored man known as Saki spoke to the other with a baritone voice that sounded out an air of authority exceeding that of Vizioso's. "You can also be brought up on kidnapping charges. You have no choice. Let him go."

"Not possible," Vizioso objected curtly. "Doctor Farrell wants political asylum from us, and we have his signed affidavit."

"What?" Saki growled under his face plate.

"I don't have to explain. My country has the right in accordance with international law to offer anyone protection and safe passage." As Vizioso spoke, he waved his chicken leg around nonchalantly in a snide manner. "The affidavit is at the embassy. I'll send a copy to your head administration in a couple of days."

"Vizioso, do not go through with this. If you do, you will be detained and prosecuted upon returning here."

"I'm warning you to watch your comments." Vizioso shot back. He straightened his posture and readjusted his tie. "You should know: our country is a peace-loving democracy."

 ** _"Of course it is!"_**

Both Saki and Vizioso stiffened at the sound of a sudden unknown voice that came out of nowhere, swinging around to the window which had a holographic display of fish projected on the glass. Immediately, the window shattered only for Vizioso to suddenly fly into the wall back first. Some of the black clad soldiers with Saki saw that Vizioso had been pinned to the wall by what seemed to be throwing stars lodged through his sleeves, jacket hems, and pant-legs. A split second after, the stars suddenly exploded with a white smoke, and when the smoke dissipated, revealed Vizioso covered in a slimy adhesive substance while remaining stuck to the wall. It would appear to the Oroku-division that if they were planning on arresting Vizioso on the spot, someone just saved them the trouble of actually detaining him themselves. But any notion of gratitude did not mean much in the heat of the moment. Since the exploding cloud of smoke happened to knock Oroku Saki off his feet, he had to get himself back upright.

"The window! Attack!" Saki yelled to his Foot soldiers as he got his bearings. The Foot soldiers in turn threw out stars of their own, aiming at the entire row of windows. The thrown stars managed to shatter every pane of glass besides the one that the mysterious attacker launched stars through to incapacitate Dominic Vizioso. Saki shortly dashed to the now glassless window with his gauntlet blades unsheathed. A few other Foot soldiers quickly followed alongside Saki with their bladed weapons drawn as he got to the window's edge. He looked down just in time to spot the mysterious assailant falling down rapidly to the streets below from where he stood. As his eyes lingered upon the person, that person (with her red hair and black tracksuit) took out a smoke bomb and crushed it in her hand, releasing a puff of smoke. The cloud of smoke left behind was thick, but it quickly began to disperse. Any Foot soldier present would have concluded that she performed the standard ninja's disappearing act, but Saki took the time to watch her a little longer. Narrowing his vision to look past the smoke screen, he could spot the redhead beginning to blend into the busy streets he was viewing from above. It seemed like she was becoming more and more transparent, and the rippling texture occurring on her body made him do a double take, not limited to blinking extra hard. But his eyes did not fool him, for that was exactly what the redheaded girl was trying to do.

"I don't believe it," Saki whispered in amazement, "psionic camouflage."

The redhead was looking up right back at him, and she gave a mischievous smile as she waved her camouflaged hand over her still-visible face, which then became invisible like the rest of her body as soon as her hand finally passed over.

* * *

 ***Suzu bells ringing***


	2. Making of a Mutant

***I'd recommend listening to Kenji Kawai's "Making of Cyborg" for this chapter. Really sets the mood.**

* * *

It was a quiet and concentrated time in a lab at TCRI. In a spacious cylindrical tank of fluid, a clump of cells was gradually growing into a system of tissues. Outside the tank, a pink brain-like alien, otherwise known as an Utrom, worked at some buttons at a control console while seated on a floating module. On a nearby computer monitor, data texts were displayed beside a digitized diagram of the tiny cell mass that was floating in the tank standing a distance away from it. The Utrom working at the console examined the systems detailing the rising percentage of human DNA. Eyes then shifted over to a smaller digital box awaiting the command to begin melding of Utrom genetic material. A tentacle rose over the keyboard and after a slight lingering, pressed the Enter-key.

The command now issued through the console caused some automated limbs to shift towards the suspended clump of tissue. Each of the limbs extended attached syringes towards the fleshy thing, with the pointed and deceptively thin but hollow needles inching closer with slow but precise aim. The needles softly sank into the thing's flesh, and pistons within the syringes' tubes pushed down a variety of pink, purple, and other variously colored substances. The little clump of cells shortly began to pulse with little sparks of light and bulged in several directions as it began to expand and develop distinguished parts.

The computer monitors immediately began to show two DNA labels with rapidly rising percentages, in which one was human while the other was Utrom. There were a few alternations, with the human genetic level rising quicker than the Utrom level, then vice-versa, and then both eventually developed at the same speed and level.

Beyond what was currently happening, more Utroms were flying by while doing their work, though they were also accompanied by colleagues of different forms and species. A human and a mutant scientist were waiting by another cylindrical tank, though it only had fluid but no other contents. At the same time, a developing embryo was gestating within its own tank while that tank was slowly being transported to another part of the laboratory via an energized railing. The tank was inched towards a circular base, in which it then became secured in the socket. The top cap of the tank extended upward to connect with the bottom half of the tank above, which happened to be the tank observed by the aforementioned human and mutant scientists. A hissing hum emanated from the two tanks and the little developing embryo was gradually floating upwards. As it rose, it passed through the ring of metal connecting the two tanks and floated into the second top tank. The thing that was once a clump of cells was now something vaguely humanoid. To be precise, there is now a bean-shaped life form with a bloated protrusion that had two faintly black spots giving the impression of eyes. There were also faint signs of pinkish streaks behind the eye-like spots. The rest of it began sprouting four thin nubs.

The four nubs had begun to grow longer and thicker, and the tips began to sprout nubs of their own. An Utrom scientist accompanying his fellow scientists observed the growing creature from both the tank glass and computer screens. At the same time, a few other Utroms in robotic walkers, both in bare robot form and in android form, were traversing the floors of the lab preparing other lab equipment for handling the embryo's development. One scientist activated a second syringe which gently prodded the embryo to inoculate another formula. Upon injection, the embryo grew a gelatinous layer around itself which served to provide it with extra nutrients as well as buffer its most delicate parts from any possible damage, whether from getting jostled against the tank glass or disturbed by an unnecessary current of fluid.

The embryo continued to grow and grow, becoming more human-shaped as each part developed to proper proportions. A computer monitor showed a scan of its growing brain, which pulsed and slowly expanded in size. Numbered digits that also showed up on the screen were rapidly rising to show an astounding development in the brain's psychic waves. A mutant scientist observing the phenomenon commented on it to an accompanying Utrom scientist piloting an android mech. In fact, as they were talking, a nearby tray of tools slightly rattled, with the noise getting one Utrom to notice.

The embryo, now having become a more full-fledged fetus, emitted a pulse of light in its head that almost appeared to be a heartbeat. Somehow, this pulsing wave caused the fetus to shed the outer membrane encasing it, but it was even strong enough to cause the glass making up its tank to clang loudly, making a few observers jump back. Everyone present took care to record the data.

The tank carrying the fetus was now transferring it down to another tank sitting below. The new tank now containing the fetus travelled along another energized rail to a large module that physically resembled a security scanner, except that it was larger and did more than just scan the condition of its contents. As the machine did its work with the tank within, the fetus grew more and more pronounced, its pinkish markings gone due to the skin having finally lost its transparency. At that point, there was now finally a fully developed infant with all the proper proportions one would see in a normal human baby.

A screen on one the side of the giant device was monitored by another mutant scientist, recording data on the stabilizing of the infant's bodily functions as well as its brain functions, keeping special note of energy input and signature emitted from the baby's brain. As expected, everything was stable, so the baby was in healthy weight and shape, as well as having a stable brain despite the tremendous amount of energy it produced only several hours before.

The tank holding the fully formed baby made its way across one final energized railway to stop underneath an open lab space above. The tank happened to be transported into a silo-like structure filled with liquid, so that when it opened, the baby drifted out and floated its way to the surface at the top of the silo. An Utrom carefully operated a control panel that caused a set of mechanical arms to descend into the liquid in which the baby was floating upwards in. With slow and careful precision, the arms carefully scooped up the baby and lifted it out of the liquid in the silo.

Once the baby was safely transported away from the pool, a female human scientist stepped forward to scoop the little one in her arms. She managed to get the baby dried by means of an installed gadget that worked similarly to a hairdryer. Once that was done, she carried the baby to a different part of the facility where she finally placed the infant into a bassinet and installed a clear cover for incubation. Throughout all of this, the baby remained asleep. On the bassinet was a label on which was written the baby's newly given name: **April O'Neil**.

* * *

In a darkened room, April O'Neil opened her eyes, having just awoken from a night's slumber. She lied there for a moment, apparently staring into nowhere with nothing to hear but her own quiet breathing. Diverting her eyes to her hand which lay limply in front of her face, she twitched her fingers and then slowly curled them inward and outward, having them get used to the feeling of movement again. She stared at her hand in contemplation, wondering if there was anything unusual about it, or if she was seeing something that wasn't there.

She lifted herself up so that she was now sitting on her bed, rubbing her eyes to make herself more awake. Flipping a switch, she opened the shutters on her window to allow a surge of sunlight to flood into her room. She gazed outside to glance at the busy streets of New York City. Aside from the burgeoning towers of steel and concrete of uniquely intricate designs, she only stared outside without even once turning her head, only focusing on getting her eyes used to the brightness for the day forward.

Once several seconds of all that passed, April planted her feet on the floor and stood up, getting off her bed. Rubbing a hand through her red hair, she made her way to the nearby bathroom to freshen up, going through the normal morning routines expected of the average human being. She then went to her closet to go through her wardrobe, but made sure not to spend any more than five minutes as opposed to how people usually did, at least ones like her if there were any. Once she was finally dressed, she made her way to her bedroom door to leave and make her way out of her home. The window in front of her bed which showed the cityscapes of New York lingered open for a while, from where one could see not just all the windows on the tallest buildings, but even the elevated platforms that held other residences and gardens of botanical innovation along with decorated support pillars holding up every architectural detail ever built above the ground level. As it was daytime, the city's usual holographic advertisements were not seen as well, but they still played no matter the time. In a way, the city looked a lot simpler when the sun is up.

But of course, the beauty of New York's sleeplessness could only be found at night, and just as one must eventually turn the lights out before leaving, the day must eventually leave to make way for the night. As April prepared to leave her home to go to her work, she flipped a switch that caused her open sunlit window to close its shutters again. She closed her door and the room once again returned to the darkness.


	3. Talks

**Location: Earth Protection Force HQ, Manhattan, New York City**

 **Time: Morning**

A large transport helicopter was hovering over the helipad on the rooftop of a tall building of fortified and near-featureless walls of concrete. It slowly descended onto the pad with a gentle grace despite the loud chopping sounds of the spinning blades levitating it. A side door opened and deployed a set of stairs that helped connect the passenger deck with the helipad itself. Out of the door, a man dressed in military garb stepped out of the plane and made his way down the steps. As he proceeded, he looked up to find someone standing at the bottom waiting for him: a tall bipedal rat of brown fur and white patterns marking facial details. A dark reddish burgundy robe draped around the rat's chest and reached down to just above his hand-like feet. On his back was a dark red sigil that resembled a flower, with each petal dotted with a circle of lighter hues.

"Hamato Yoshi, what a surprise," the man greeted loudly, having to shout over the noise of the helicopter's blades.

"General Griffin," the rat known as Hamato Yoshi replied in turn, bowing his head and arching his back forward slightly in respect.

"This must be important if you went through the trouble to see me yourself," Griffin quipped. "Come with me. We'll go somewhere quieter."

* * *

The two calmly and patiently stood side by side as they rode the elevator down, taking in the view of the city through the full glass pane in front of them.

"So what brings the patriarch of the Hamato-Division to the Earth Protection Force headquarters?" Griffin spoke up.

Yoshi was brief and direct. "I need to ask you about the secret talk set to take place in Tokyo tomorrow."

"Procedural as always," Griffin huffed quietly. "Well, the Triceraton regime that took over Sectoid 1 after the revolution demands financial aid, supposedly for colonization efforts. They boast of moderation, but they're no better than the last lot. Now they feel entitled to funds because of our own history in exploitation. Somebody hand these guys a mirror…"

"What is the Earth Protection Force going to do?"

"Well, there's a problem. The former leader of the Vreen that controlled the hive planet is here seeking political asylum."

"You mean Lord Dregg, correct?"

"Yes, and that means we either deny the Triceratons the funds and treat Dregg as a political refugee or help them and kick him out." Griffin turned slightly to look Yoshi in the eye, prompting the rat to do the same. Griffin continued, "Personally, I'm inclined to deport him, forcibly if necessary, but I'd have to come up with a politically acceptable reason for it."

Yoshi, briefly taking a moment to process the general's words, turned his head away to look back out to the cityscapes. The elevator stopped gently, having reached its destination. As the double doors on the other side slid open, Griffin proceeded to walk out, but stopped short of the doors to briefly turn back to Yoshi.

"By the way, I want to thank you for your help with that other political asylum situation. Oroku Saki from the Oroku-Division wasn't so grateful. But you realize that we in the diplomat business must avoid messy situations." He turned back to leave the elevator, leaving Yoshi to keep his eyes on the general's back until the doors closed again. As the elevator resumed its descent, Yoshi returned to gazing through the tall window.

 _"_ _Messy situations,"_ he thought to himself, leaning an arm against the rail separating him from the glass. _"Why did Saki have to involve himself in this way again?"_

* * *

 ***My apologies for the extended delay. Other things (aka-life) just got in the way and I just had a hard time mustering the will to keep going. Hopefully it won't be the case further down the line. Hope you liked the chapter!**


End file.
